Not sure if this is also happening on other maps, but there are missions on New England Mountains and Emerald Coast that require you to be holding the weapon used when harvesting the animal in order for you to complete the missions. This seems to be a bug because you don't have to do this on other missions and there are no mission instructions informing you that this is a requirement. I only found out how to resolve the issue by googling the error online and asking in discord.
A lot of time and practise goes into completing some of the more difficult missions, so it can be frustrating when you eventually fulfil the requirements but don't pass the checks.